fix logic for class assignment based on zscores in biosample activity…

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weng-lab · Oct 4, 2024 · 520398d · 520398d
1 parent b395428
commit 520398d
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Showing 4 changed files with 8,752 additions and 12,336 deletions.
diff --git a/screen2.0/src/app/search/_ccredetails/ccredetails.tsx b/screen2.0/src/app/search/_ccredetails/ccredetails.tsx
@@ -117,7 +117,7 @@ export const CcreDetails: React.FC<CcreDetailsProps> = ({ accession, region, ass
       })].sort((a, b) => a.distanceToTSS - b.distanceToTSS).slice(0, 3)
     } : null
   }, [dataNearbyAndLinked, region])
-
+console.log("nearest3AndLinkedGenes",nearest3AndLinkedGenes && nearest3AndLinkedGenes.nearbyGenes.sort((a,b)=>a.distanceToTSS-b.distanceToTSS))
   //Used to pass genes and their linking method to Gene Expression and RAMPAGE pages
   const uniqueGenes: { name: string; linkedBy: string[]; }[] = useMemo(() => {
     const uniqueGenes: { name: string; linkedBy: string[]; }[] = [];
@@ -154,8 +154,8 @@ export const CcreDetails: React.FC<CcreDetailsProps> = ({ accession, region, ass
         <Typography variant="h6">{`${region.chrom}:${region.start.toLocaleString("en-US")}-${region.end.toLocaleString("en-US")}`}</Typography>
       </Stack>
       <Divider sx={{ mb: 2 }} />
-      {page === 0 &&
-        <InSpecificBiosamples accession={accession} assembly={assembly} />
+      {page === 0 && nearest3AndLinkedGenes &&
+        <InSpecificBiosamples accession={accession} assembly={assembly} distanceToTSS={nearest3AndLinkedGenes.nearbyGenes.sort((a,b)=>a.distanceToTSS-b.distanceToTSS)[0].distanceToTSS}/>
       }
       {(page === 1 && assembly !== "mm10") &&
         (loadingLinkedGenes ?

diff --git a/screen2.0/src/app/search/_ccredetails/inspecificbiosample.tsx b/screen2.0/src/app/search/_ccredetails/inspecificbiosample.tsx
@@ -22,6 +22,7 @@ export type cCRERow = {
 type InSpecificBiosamplesProps = {
   accession: string,
   assembly: "GRCh38" | "mm10",
+  distanceToTSS: number
 }
 
 
@@ -166,7 +167,7 @@ const ctAgnosticColumns = () => [
 ]
 
 //Cache is not working as expected when switching between open cCREs
-export const InSpecificBiosamples: React.FC<InSpecificBiosamplesProps> = ({ accession, assembly }) => {
+export const InSpecificBiosamples: React.FC<InSpecificBiosamplesProps> = ({ accession, assembly, distanceToTSS }) => {
 
   const { data: data_toptissues, loading: loading_toptissues, error: error_toptissues } = useQuery(TOP_TISSUES,
     {
@@ -190,6 +191,8 @@ export const InSpecificBiosamples: React.FC<InSpecificBiosamplesProps> = ({ acce
   )
 
 
+  const distance  = distanceToTSS
+
 
   let partialDataCollection: cCRERow[], coreCollection: cCRERow[], ancillaryCollection: cCRERow[];
   if (data_toptissues) {
@@ -278,44 +281,60 @@ export const InSpecificBiosamples: React.FC<InSpecificBiosamplesProps> = ({ acce
       }
     })
 
-    let igroup = data_toptissues?.cCREQuery[0]?.group
+
 
     let ccreCts = typedata.map((t) => {
-      let group = igroup      
-      if (t.dnase <= 1.64 && t.dnase != -11.0) group = "ylowdnase"
-      if (igroup == "PLS") {
-        if (t.h3k4me3 > 1.64) group = "PLS"
-        if (t.h3k27ac > 1.64) group = "pELS"
+      let group     
+      let tf =  data_ccre_tf && data_ccre_tf.getcCRETFQuery.length>0 ? data_ccre_tf.getcCRETFQuery.find(a=> t.ct===a.celltype)?.tf.toString(): undefined     
 
-      } else {
-        if (t.h3k27ac > 1.64) {
-          if (igroup === "pELS") {
-            group = "pELS"
-          } else {
-            group = "dELS"
+      if(t.dnase != -11.0)
+      {
+          if((t.dnase >= 1.64)) {
+            if(t.h3k4me3 >= 1.64) {
+                if(distance <= 200) {
+                    group = "PLS" //Promoter-like signatures (promoter) must fall within 200 bp of a TSS and have high chromatin accessibility and H3K4me3 signals.
+                }
+                else if((t.h3k27ac < 1.64) && distance > 200) {
+                        group = "CA-H3K4me3" //Chromatin accessibility + H3K4me3 (CA-H3K4me3) have high chromatin accessibility and H3K4me3 signals but low H3K27ac signals and do not fall within 200 bp of a TSS.
+                }
+                else if (distance <= 2000  && t.h3k27ac >= 1.64) {              
+                        group = "pELS" //Enhancer-like signatures (enhancer) have high chromatin accessibility and H3K27ac signals. Enhancers are further divided into TSS-proximal or distal with a 2 kb distance cutoff.          
+                } else if(distance > 2000  && t.h3k27ac >= 1.64) {              
+                        group = "dELS" //Enhancer-like signatures (enhancer) have high chromatin accessibility and H3K27ac signals. Enhancers are further divided into TSS-proximal or distal with a 2 kb distance cutoff.          
+                }
+            }
+            else if(t.h3k27ac >= 1.64) {
+                if(distance <= 2000) {   
+                        group ="pELS"       //Enhancer-like signatures (enhancer) have high chromatin accessibility and H3K27ac signals. Enhancers are further divided into TSS-proximal or distal with a 2 kb distance cutoff.          
+                } else if(distance > 2000) {
+                        group = "dELS"  //Enhancer-like signatures (enhancer) have high chromatin accessibility and H3K27ac signals. Enhancers are further divided into TSS-proximal or distal with a 2 kb distance cutoff.          
+                }
+            }
+            else if(t.ctcf >= 1.64) {
+                group = "CA-CTCF" //Chromatin accessibility + CTCF (CA-CTCF) have high chromatin accessibility and CTCF signals but low H3K4me3 and H3K27ac signals.
+            }
+            else if(tf==='1') {
+                group = "CA-TF" //Chromatin accessibility + transcription factor (CA-TF) have high chromatin accessibility, low H3K4me3, H3K27ac, and CTCF signals and are bound by a transcription factor.
+            }
+            else {
+                group = "CA" //Chromatin accessibility (CA) have high chromatin accessibility, and low H3K4me3, H3K27ac, and CTCF signals.
+            }
           }
-        }
-        if (t.h3k4me3 > 1.64) group = "CA-H3K4me3"
-      }
-      if (t.ctcf > 1.64) group = "ctcf"
-      if (-11.0 === t.dnase) group = "zunclassified"
-      if (t.dnase > 1.64) {
-        group = "dnase"
-        if (t.h3k27ac > 1.64) {          
-          if (igroup === "pELS") {
-            group = "pELS"
-          } else if(igroup === "PLS") {
-            group = "PLS"
-          } 
-          else {
-            group = "dELS"
+          else {            
+            if(tf==='1'){
+              group = "TF" //Transcription factor (TF) have low chromatin accessibility, low H3K4me3, H3K27ac, and CTCF signals and are bound by a transcription factor.
+            } else {
+              group = "InActive" //low chromatin accessibility, low H3K4me3, H3K27ac, and CTCF signals and are NOT bound by a transcription factor.
+            }            
           }
-        }
-      } else {
-        group = "ylowdnase"
       }
-
-
+      else {
+        group  = "noclass" //If not active in DNase, No class assigned
+      }
+
+
+      console.log(t.celltypename, t.atac, t.dnase,t.h3k27ac,t.h3k4me3,t.ctcf, tf, group)
+
       let type: "core" | "partial" | "ancillary"
 
       type = "ancillary"

diff --git a/screen2.0/src/app/search/_ccredetails/utils.tsx b/screen2.0/src/app/search/_ccredetails/utils.tsx
@@ -177,8 +177,8 @@ export const GROUP_COLOR_MAP: Map<string, string> = new Map([
   ["pELS","Proximal Enhancer:#FFA700"],
   ["dELS","Distal Enhancer:#FFCD00"],
   ["PLS","Promoter:#ff0000"],    
-  ["ylowdnase","Low DNase:#8c8c8c"],
-  ["zunclassified","zunclassified:#8c8c8c"]  
+  ["noclass","noclass:#8c8c8c"],
+  ["InActive","In Active:#8c8c8c"]  
 ])
 
 type Coordinates = {